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- PDB-3o2r: Structural flexibility in region involved in dimer formation of n... -

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Basic information

Entry
Database: PDB / ID: 3o2r
TitleStructural flexibility in region involved in dimer formation of nuclease domain of Ribonuclase III (rnc) from Campylobacter jejuni
Components(Ribonuclease III) x 2
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / nuclease domain / ribonuclase III
Function / homology
Function and homology information


ribonuclease III / ribonuclease III activity / tRNA processing / mRNA processing / rRNA processing / double-stranded RNA binding / regulation of gene expression / rRNA binding / metal ion binding / cytoplasm
Similarity search - Function
Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif ...Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Ribonuclease-III-like / Ribonuclease III / Ribonuclease III family signature. / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.251 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Structural Flexibility in Region Involved in Dimer Formation of Nuclease Domain of Ribonuclase III (rnc) from Campylobacter jejuni.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 30, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease III
B: Ribonuclease III
C: Ribonuclease III
D: Ribonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7158
Polymers76,5734
Non-polymers1424
Water17,529973
1
A: Ribonuclease III
B: Ribonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3584
Polymers38,2872
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-41 kcal/mol
Surface area13200 Å2
MethodPISA
2
C: Ribonuclease III
D: Ribonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3584
Polymers38,2872
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-41 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.451, 61.552, 118.093
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease III


Mass: 19136.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: CJSA_1547, rnc / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 (Magic)
References: UniProt: D3FPA5, UniProt: Q9PM40*PLUS, ribonuclease III
#2: Protein Ribonuclease III


Mass: 19149.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: CJSA_1547, rnc / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 (Magic)
References: UniProt: D3FPA5, UniProt: Q9PM40*PLUS, ribonuclease III
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 973 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIN CHAINS B AND D, RESIDUE 31 DISPLAYS MICROHETEROGENEITY AND APPEARS AS BOTH A METHYLATED LYSINE ...IN CHAINS B AND D, RESIDUE 31 DISPLAYS MICROHETEROGENEITY AND APPEARS AS BOTH A METHYLATED LYSINE AND LYSINE. THE ORIGINAL SEQUENCE WAS THE 224 RESIDUES AS FOUND IN THE UNIPROT ENTRY - BUT THE AUTHORS SEE A CLEAR TRUNCATION AT 164.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4
Details: Protein solution: 7.6 mg/mL, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen solution: PACT (B1), 0.1M MIB buffer pH 4.0, 25% w/v PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 3, 2010 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.25→30 Å / Num. all: 151202 / Num. obs: 151202 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.4
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.6 / Num. unique all: 7499 / % possible all: 99.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N3W

3n3w


Resolution: 1.251→29.78 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.866 / SU ML: 0.018 / Isotropic thermal model: Isotropic Individually refined / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1683 7589 5 %RANDOM
Rwork0.13327 ---
all0.13501 143537 --
obs0.13501 143537 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.409 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å20.05 Å2
2---0.78 Å2-0 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.251→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4558 0 4 973 5535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225414
X-RAY DIFFRACTIONr_bond_other_d0.0010.023703
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9837382
X-RAY DIFFRACTIONr_angle_other_deg0.89139191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0415725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3825.843255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.452151046
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0211514
X-RAY DIFFRACTIONr_chiral_restr0.0780.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026304
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021082
X-RAY DIFFRACTIONr_mcbond_it1.5511.53316
X-RAY DIFFRACTIONr_mcbond_other1.9331.51329
X-RAY DIFFRACTIONr_mcangle_it2.325394
X-RAY DIFFRACTIONr_scbond_it3.53632098
X-RAY DIFFRACTIONr_scangle_it5.1454.51973
X-RAY DIFFRACTIONr_rigid_bond_restr1.71635414
LS refinement shellResolution: 1.251→1.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 546 -
Rwork0.185 10625 -
obs-10625 99.55 %

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